Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade.

Background Chikungunya virus (CHIKV) is a re-emerging arbovirus associated with sporadic outbreaks in Cameroon since 2006. We generated viral whole genomes to analyse the origins of evolutionary lineages, potential of emergence/re-emergence and infer transmission dynamics of recent Cameroon CHIKV outbreak strains. Methods Samples collected between 2016-2019 during CHIKV outbreaks in Cameroon were screened for CHIKV using reverse transcription polymerase chain reaction (RT-PCR), followed by whole genome sequencing of positive samples. Results Three coding-complete CHIKV genomes were obtained from samples which belong to an emerging sub-lineage of the East/Central/South African genotype and formed a monophyletic taxon with previous Central African strains which we have named the new Central African clade, and appears to be evolving at 3.0 × 10-4 nucleotide substitutions per site per year (95% HPD interval of 1.94 × 10-4 and 4.1 × 10-4). Notably, mutations in the envelope proteins (E1-A226V, E2-L210Q, and E2-I211T), which are known to enhance CHIKV adaptability and infectious potential in Aedes albopictus, were present in all strains and mapped to established high-density Ae. albopictus populations. Conclusions These new CHIKV strains constitute a conserved genomic pool of an emerging sub-lineage, reflecting a putative vector host adaptation to Ae. albopictus, which has practically displaced Ae. aegypti from select regions of Cameroon.